{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import patternTransitions as p\n",
    "from itertools import repeat\n",
    "import seaborn as sns\n",
    "import matplotlib.pyplot as plt\n",
    "from mpl_toolkits.mplot3d import Axes3D\n",
    "import common.seg as seg\n",
    "import _pickle as cPickle\n",
    "import common.lin as lin\n",
    "import aniso\n",
    "import numpy as np\n",
    "import matplotlib.ticker as ticker"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#load FM1 at specified timepoints\n",
    "tss, linss = lin.mkSeries1(d=\"../data/FM1/tv/\",\n",
    "                           dExprs=\"../data/geneExpression/\",\n",
    "                           linDataLoc=\"../data/FM1/tracking_data/\",\n",
    "                           ft=lambda t: t in {10, 40, 96, 120, 132})\n",
    "lin.filterL1_st(tss)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "def mkViolinPlot(d, ax, ws=0.7, vert=False):\n",
    "    xs_labs = sorted(d.keys())\n",
    "    xs = range(len(xs_labs))\n",
    "    ys = [d[x] for x in xs_labs]\n",
    "    \n",
    "    ax.yaxis.set_major_locator(ticker.MultipleLocator(0.05))\n",
    "    sns.set_style(\"whitegrid\", {'grid.linestyle':'--'})\n",
    "    ax.set_xticks(xs)\n",
    "    ax.set_xticklabels(xs_labs)\n",
    "    violin_parts = ax.violinplot(ys, xs, showmeans=True, widths=ws)\n",
    "    \n",
    "    for pc in violin_parts['bodies']:\n",
    "        pc.set_facecolor(\"#f5d742\")\n",
    "        pc.set_edgecolor('black')\n",
    "\n",
    "    for partname in ('cbars','cmins','cmaxes','cmeans'):\n",
    "        vp = violin_parts[partname]\n",
    "        vp.set_edgecolor('red')\n",
    "        vp.set_linewidth(0.5)\n",
    "    \n",
    "    if vert:\n",
    "        plt.xticks(rotation=90)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Per pattern"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import grates as grs\n",
    "\n",
    "G = p.mkTGraphN()\n",
    "grates = grs.grates_avg_cons(tss, linss)\n",
    "grates_pats = p.addCombPatterns(grates, tss)\n",
    "\n",
    "grs_state = p.getGAnisosPerPattern(G, grates_pats)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "plt.rcParams.update({'font.size': 12})\n",
    "fig = plt.figure(figsize=(12, 5.5))\n",
    "ax = fig.add_subplot('111')\n",
    "\n",
    "ax.set_xlabel(\"cell state\")\n",
    "ax.set_ylabel(r'growth rate ($h^{-1}$)')\n",
    "ax.set_ylim((-0.05, 0.15))\n",
    "ax.yaxis.set_ticks(np.arange(-0.05, 0.15, 0.1))\n",
    "ax.yaxis.set_major_locator(ticker.MultipleLocator(0.1))\n",
    "\n",
    "mkViolinPlot(grs_state, ax)\n",
    "\n",
    "fout = \"state_growth_rates.png\"\n",
    "plt.savefig(fout, dpi=300, bbox_inches='tight')\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Per pattern on graph"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "p.addGRates(G, grates_pats) "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "p.drawTGraph(G, p.gr)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Per gene"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import patternTransitions as p\n",
    "grates_gene = p.getGAnisosPerGene(tss, grates)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "fig = plt.figure(figsize=(10, 5))\n",
    "ax = fig.add_subplot('111')\n",
    "\n",
    "ax.set_xlabel(\"gene\")\n",
    "ax.set_ylabel(r'growth rate ($h^{-1}$)')\n",
    "ax.set_ylim((-0.1, 0.2))\n",
    "ax.yaxis.set_ticks(np.arange(-0.1, 0.2, 0.1))\n",
    "ax.yaxis.set_major_locator(ticker.MultipleLocator(0.1))\n",
    "\n",
    "mkViolinPlot(grates_gene, ax, vert=True)\n",
    "\n",
    "fout = \"gene_grates.png\"\n",
    "plt.savefig(fout, dpi=300, bbox_inches='tight')\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Per gene, per stage"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "def tToStage(t):\n",
    "    if t==10: return 0\n",
    "    elif t==40: return 1\n",
    "    elif t==96: return 2\n",
    "    elif t==120: return 3\n",
    "    elif t==132: return 4"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "grates_gene_time = p.getGAnisosPerGeneTime(tss, grates)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "for t in sorted(grates_gene_time.keys()):\n",
    "    fig = plt.figure(figsize=(10, 5))\n",
    "    ax = fig.add_subplot('111')\n",
    "    \n",
    "    ax.set_title(\"stage {t}\".format(t=tToStage(t)))\n",
    "    ax.set_xlabel(\"gene\")\n",
    "    ax.set_ylabel(r'growth rate ($h^{-1}$)')\n",
    "    ax.set_ylim((-0.05, 0.15))\n",
    "    ax.yaxis.set_major_locator(ticker.MultipleLocator(0.1))\n",
    "\n",
    "    mkViolinPlot(grates_gene_time[t], ax, ws=0.4, vert=True)\n",
    "\n",
    "    fout = \"gene_growth_{t}.png\".format(t=t)\n",
    "    plt.savefig(fout, dpi=300, bbox_inches='tight')\n",
    "    plt.show()"
   ]
  }
 ],
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